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(-) Description

Title :  CRYSTAL STRUCTURE OF GALACOSYLTRANSFERASE LGTC IN COMPLEX WITH DONOR AND ACCEPTOR SUGAR ANALOGS.
 
Authors :  K. Persson, H. D. Ly, M. Diekelmann, W. W. Wakarchuk, S. G. Withers, N. C. J. Strynadka
Date :  29 Nov 00  (Deposition) - 14 Feb 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Beta Protein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Persson, H. D. Ly, M. Dieckelmann, W. W. Wakarchuk, S. G. Withers, N. C. Strynadka
Crystal Structure Of The Retaining Galactosyltransferase Lgtc From Neisseria Meningitidis In Complex With Donor And Acceptor Sugar Analogs.
Nat. Struct. Biol. V. 8 166 2001
PubMed-ID: 11175908  |  Reference-DOI: 10.1038/84168
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GALACTOSYL TRANSFERASE LGTC
    Chains: A
    EC Number: 2.4.1.44
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PCW
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: LGTC
    Mutation: YES
    Organism Scientific: NEISSERIA MENINGITIDIS
    Organism Taxid: 487

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1DEL1Ligand/Ion4-DEOXYLACTOSE
2MN1Ligand/IonMANGANESE (II) ION
3MSE7Mod. Amino AcidSELENOMETHIONINE
4UPF1Ligand/IonURIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUOROGALACTOSE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:76 , HIS A:78 , ASP A:130 , VAL A:133 , GLN A:189 , PRO A:211 , CYS A:246 , GLY A:247 , UPF A:501 , HOH A:601 , HOH A:752 , HOH A:767BINDING SITE FOR RESIDUE DEL A 500
2AC2SOFTWAREASP A:103 , ASP A:105 , HIS A:244 , UPF A:501BINDING SITE FOR RESIDUE MN A 400
3AC3SOFTWAREALA A:6 , ALA A:7 , ASP A:8 , ASN A:10 , TYR A:11 , HIS A:78 , ILE A:79 , SER A:80 , THR A:83 , ARG A:86 , ASP A:103 , ILE A:104 , ASP A:105 , ASN A:153 , ALA A:154 , GLY A:155 , TYR A:186 , GLN A:187 , ASP A:188 , GLN A:189 , HIS A:244 , CYS A:246 , GLY A:247 , LYS A:250 , MN A:400 , DEL A:500 , HOH A:628 , HOH A:790BINDING SITE FOR RESIDUE UPF A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1GA8)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Mse A:238 -Pro A:239

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GA8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1GA8)

(-) Exons   (0, 0)

(no "Exon" information available for 1GA8)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:278
 aligned with P96945_NEIME | P96945 from UniProtKB/TrEMBL  Length:311

    Alignment length:282
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280  
         P96945_NEIME     1 MDIVFAADDNYAAYLCVAAKSVEAAHPDTEIRFHVLDAGISEANRAAVAANLRGGGGNIRFIDVNPEDFAGFPLNIRHISITTYARLKLGEYIADCDKVLYLDIDVLVRDSLTPLWDTDLGDNWLGACIDLFVERQEGYKQKIGMADGEYYFNAGVLLINLKKWRRHDIFKMSCEWVEQYKDVMQYQDQDILNGLFKGGVCYANSRFNFMPTNYAFMANWFASRHTDPLYRDRTNTVMPVAVSHYCGSAKPWHRDCTAWGAERFTELGGSLTTVPEEWRGKL 282
               SCOP domains d1ga8a_ A: Galactosyltransferase LgtC                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -1ga8A00 A:2-282 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeehhhhhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhhhhhhhhhh..eeeee.hhhhhh.........hhhhhhhhhhhhhh.....eeee...eee...hhhhhh.......eeeeehhhhhh..hhhhhh........eeeeeeeehhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhh..eeeehhhhh.hhhhhhh.----.....hhhhhhhhh......eee................hhhhhhhhh.....hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ga8 A   1 mDIVFAADDNYAAYLCVAAKSVEAAHPDTEIRFHVLDAGISEANRAAVAANLRGGGGNIRFIDVNPEDFAGFPLNIRHISITTYARLKLGEYIADCDKVLYLDIDVLVRDSLTPLWDTDLGDNWLGASIDLFVERQEGYKQKIGmADGEYYFNAGVLLINLKKWRRHDIFKmSSEWVEQYKDVmQYQDQDILNGLFKGGVCYANSRFNFmPTNYAFm----ASRHTDPLYRDRTNTVmPVAVSHYCGPAKPWHRDCTAWGAERFTELAGSLTTVPEEWRGKL 282
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140    |  150       160       170 |     180   |   190       200       210      |  - |     230       240       250       260       270       280  
                            |                                                                                                                                             145-MSE                    172-MSE     184-MSE                   210-MSE  |  222             238-MSE                                        
                            1-MSE                                                                                                                                                                                                                 217-MSE                                                             


Chain A from PDB  Type:PROTEIN  Length:278
 aligned with Q93EK7_NEIME | Q93EK7 from UniProtKB/TrEMBL  Length:311

    Alignment length:282
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280  
         Q93EK7_NEIME     1 MDIVFAADDNYAAYLCVAAKSVEAAHPDTEIRFHVLDAGISEANRAAVAANLRGGGGNIRFIDVNPEDFAGFPLNIRHISITTYARLKLGEYIADCDKVLYLDIDVLVRDSLTPLWDTDLGDNWLGACIDLFVERQEGYKQKIGMADGEYYFNAGVLLINLKKWRRHDIFKMSCEWVEQYKDVMQYQDQDILNGLFKGGVCYANSRFNFMPTNYAFMANRFASRHTDPLYRDRTNTVMPVAVSHYCGPAKPWHRDCTAWGAERFTELAGSLTTVPEEWRGKL 282
               SCOP domains d1ga8a_ A: Galactosyltransferase LgtC                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -1ga8A00 A:2-282 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeehhhhhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhhhhhhhhhh..eeeee.hhhhhh.........hhhhhhhhhhhhhh.....eeee...eee...hhhhhh.......eeeeehhhhhh..hhhhhh........eeeeeeeehhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhh..eeeehhhhh.hhhhhhh.----.....hhhhhhhhh......eee................hhhhhhhhh.....hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ga8 A   1 mDIVFAADDNYAAYLCVAAKSVEAAHPDTEIRFHVLDAGISEANRAAVAANLRGGGGNIRFIDVNPEDFAGFPLNIRHISITTYARLKLGEYIADCDKVLYLDIDVLVRDSLTPLWDTDLGDNWLGASIDLFVERQEGYKQKIGmADGEYYFNAGVLLINLKKWRRHDIFKmSSEWVEQYKDVmQYQDQDILNGLFKGGVCYANSRFNFmPTNYAFm----ASRHTDPLYRDRTNTVmPVAVSHYCGPAKPWHRDCTAWGAERFTELAGSLTTVPEEWRGKL 282
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140    |  150       160       170 |     180   |   190       200       210      |  - |     230       240       250       260       270       280  
                            1-MSE                                                                                                                                         145-MSE                    172-MSE     184-MSE                   210-MSE  |  222             238-MSE                                        
                                                                                                                                                                                                                                                  217-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GA8)

(-) Gene Ontology  (3, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (P96945_NEIME | P96945)
molecular function
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).

Chain A   (Q93EK7_NEIME | Q93EK7)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        P96945_NEIME | P96945: 1g9r
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        Q93EK7_NEIME | Q93EK7: 1g9r 1ss9

(-) Related Entries Specified in the PDB File

1g9r 1G9R CONTAINS THE SAME PROTEIN IN COMPLEX WITH THE DONOR SUGAR ANALOG.